Create resource_extra_fields_export.py

examples/resource_extra_fields_export.py

@@ -0,0 +1,227 @@
+"""
+eLabFTW Resource Export Script
+--------------------------------
+
+This script connects to an eLabFTW instance via the API and exports all items
+from a specific category.
+
+For each item, the script:
+- Extracts the internal eLabFTW resource ID
+- Extracts the item title
+- Reads all configured extra fields (custom metadata fields)
+- Exports the data in a predefined column order
+
+The export is written to:
+- A CSV file (for universal compatibility)
+- An XLSX Excel file (with formatting, filters, and auto column width)
+
+The FIELD_ORDER list defines the exact column structure of the export.
+This ensures a stable and reproducible layout, which is important for:
+- Regulatory documentation
+- Data imports into other systems
+- Standardized reporting
+"""
+
+import elabapi_python
+import json
+import csv
+from openpyxl import Workbook
+from openpyxl.styles import Font
+from openpyxl.utils import get_column_letter
+
+#########################
+#        CONFIG         #
+#########################
+
+# Base URL of your eLabFTW API (must include /api/v2)
+API_HOST_URL = 'https://YOUR-URL/api/v2'
+
+# Personal API key generated in eLabFTW
+API_KEY = 'YOUR API Key'
+
+# Category ID from which items should be exported
+CATEGORY_ID = 123456
+
+# Output filenames
+OUTPUT_FILE = "export.csv"
+OUTPUT_XLSX = "export.xlsx"
+
+#########################
+#   API CONFIGURATION   #
+#########################
+
+# Create configuration object for the eLabFTW API
+configuration = elabapi_python.Configuration()
+configuration.api_key['api_key'] = API_KEY
+configuration.api_key_prefix['api_key'] = 'Authorization'
+configuration.host = API_HOST_URL
+
+configuration.debug = False
+
+# Set to True if valid SSL certificates are used
+configuration.verify_ssl = True
+
+# Create API client
+api_client = elabapi_python.ApiClient(configuration)
+
+# Set authorization header manually (required for authentication)
+api_client.set_default_header(
+    header_name='Authorization',
+    header_value=API_KEY
+)
+
+# Load Items API endpoint
+itemsApi = elabapi_python.ItemsApi(api_client)
+
+###############################
+#   DEFINE EXPORT ORDER HERE  #
+###############################
+
+"""
+FIELD_ORDER defines the exact column order of metadata fields
+in the exported files.
+
+Why is this necessary?
+
+eLabFTW stores extra fields dynamically in JSON format.
+Without explicitly defining the order:
+- Column positions could change
+- Fields might appear in random order
+- Downstream processing (e.g., Excel templates, validation scripts)
+  could break
+
+By defining FIELD_ORDER:
+- The export structure remains stable
+- Reports remain consistent
+- Future modifications can be controlled centrally
+
+You can modify this list to match your own category setup.
+Simply replace the example field names below with the exact
+field titles used in your system.
+"""
+
+FIELD_ORDER = [
+    "Record Number",            # e.g. internal running number
+    "Project ID",               # e.g. reference or file number
+    "Organism Name",            # e.g. E. coli strain
+    "Gene / Target",            # e.g. transgene or modification
+    "Storage Location",         # e.g. freezer or storage unit
+    "Experiment Purpose",       # short description of use
+    "Donor Organism",
+    "Recipient Organism",
+    "Vector",
+    "Resistance Marker",
+    "Sequence Information",
+    "Risk Assessment Reference",
+    "Created By",
+    "Created At",
+    "Comments"
+]
+
+# --------------------------------------------------
+# ----------- SCRIPT STARTS HERE ------------------
+# --------------------------------------------------
+
+print("Starting export...")
+
+# Retrieve all items from the specified category
+items = itemsApi.read_items(cat=CATEGORY_ID)
+
+print(f"Items found: {len(items)}")
+
+rows = []
+
+# Iterate through all retrieved items
+for item in items:
+
+    row = {}
+
+    # Internal eLabFTW resource ID (primary identifier)
+    row["Ressourcen ID"] = item.id or ""
+
+    # Item title
+    row["Titel"] = item.title or ""
+
+    # Metadata is stored as JSON string
+    metadata_raw = item.metadata
+
+    if metadata_raw:
+        metadata = json.loads(metadata_raw)
+        extra_fields = metadata.get("extra_fields", {})
+    else:
+        extra_fields = {}
+
+    normalized_fields = {k.strip().lower(): v for k, v in extra_fields.items()}
+
+    for field in FIELD_ORDER:
+        key = field.strip().lower()
+        if key in normalized_fields:
+            value = normalized_fields[key].get("value", "")
+        else:
+            value = ""
+
+        # Convert list-type fields into comma-separated string
+        if isinstance(value, list):
+            value = ", ".join(value)
+
+        row[field] = value
+
+    rows.append(row)
+
+#########################
+#       WRITE CSV       #
+#########################
+
+# Define final column structure
+csv_columns = ["Ressourcen ID", "Titel"] + FIELD_ORDER
+
+# Write CSV file (UTF-8 encoding for special characters)
+with open(OUTPUT_FILE, "w", newline="", encoding="utf-8") as f:
+    writer = csv.DictWriter(f, fieldnames=csv_columns)
+    writer.writeheader()
+    writer.writerows(rows)
+
+print("CSV export finished.")
+
+#########################
+#      WRITE XLSX       #
+#########################
+
+wb = Workbook()
+ws = wb.active
+ws.title = "Export"
+
+# Write header row
+ws.append(csv_columns)
+
+# Make header row bold
+for cell in ws[1]:
+    cell.font = Font(bold=True)
+
+# Write data rows
+for row in rows:
+    ws.append([row[col] for col in csv_columns])
+
+# Enable auto-filter for the entire sheet
+ws.auto_filter.ref = ws.dimensions
+
+# Automatically adjust column width based on content length
+for col in ws.columns:
+    max_length = 0
+    column = col[0].column
+    column_letter = get_column_letter(column)
+
+    for cell in col:
+        try:
+            if cell.value:
+                max_length = max(max_length, len(str(cell.value)))
+        except:
+            pass
+
+    adjusted_width = max_length + 2
+    ws.column_dimensions[column_letter].width = adjusted_width
+
+# Save Excel file
+wb.save(OUTPUT_XLSX)
+
+print("XLSX export finished successfully.")